Exploring ORFan Domains in Giant Viruses: Structure of Mimivirus Sulfhydryl Oxidase R596

PLoS ONE

Volumn 7, Issue 11, 2012, Pages

  Hakim, Motti ^a   Ezerina, Daria ^a   Alon, Assaf ^a   Vonshak, Ohad ^a   Fass, Deborah ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

DISULFIDE; DITHIOL DERIVATIVE; DOUBLE STRANDED DNA; THIOL OXIDASE; UNCLASSIFIED DRUG; VIRUS ENZYME; VIRUS ENZYME R596;

ARTICLE; BACULOVIRUS; CARBOXY TERMINAL SEQUENCE; COMPLEX FORMATION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME BINDING; ENZYME LOCALIZATION; ENZYME STRUCTURE; GENE SEQUENCE; MIMIVIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; OXIDATION REDUCTION REACTION; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN TARGETING; SEQUENCE HOMOLOGY; SIGNAL TRANSDUCTION; VIRION; VIRUS GENE; VIRUS GENOME;

CRYSTALLOGRAPHY, X-RAY; MIMIVIRIDAE; OXIDOREDUCTASES; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; VIRAL PROTEINS;

DNA VIRUSES; MIMIVIRUS;

EID: 84870344618     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0050649     Document Type: Article

References (33)

1. Ogata H, Claverie JM, (2007) Unique genes in giant viruses: regular substitution pattern and anomalously short size. Genome Res 17: 1353-1361.
2. Fischer D, Eisenberg D, (1999) Finding families for genomic ORFans. Bioinformatics 15: 759-762.
3. Renesto P, Abergel C, Decloquement P, Moinier D, Azza S, et al. (2006) Mimivirus giant particles incorporate a large fraction of anonymous and unique gene products. J Virol 80: 11678-11685.
4. Fass D, (2008) The Erv family of sulfhydryl oxidases. Biochim Biophys Acta 1783: 557-566.
5. Gross E, Sevier CS, Vala A, Kaiser CA, Fass D, (2002) A new FAD-binding fold and intersubunit disulfide shuttle in the thiol oxidase Erv2p. Nat Struct Bio. 9: 61-71.
6. Hofhaus G, Lee JE, Tews I, Rosenberg B, Lisowsky T, (2003) The N-terminal cysteine pair of yeast sulfhydryl oxidase Erv1p is essential for in vivo activity and interacts with the primary redox centre. Eur J Biochem 270: 1528-1535.
7. Hakim M, Mandelbaum A, Fass D, (2011) Structure of a baculovirus sulfhydryl oxidase, a highly divergent member of the Erv flavoenzyme family. J Virol 85: 9406-9413.
8. Hakim M, Fass D, (2010) Cytosolic disulfide bond formation in cells infected with large nucleocytoplasmic DNA viruses. Antioxid Redox Signal 13: 1261-1271.
9. Kodali VK, Thorpe C, (2010) Oxidative protein folding and the Quiescin-sulfhydryl oxidase family of flavoproteins. Antioxid Redox Signal 13: 1217-1230.
10. Hakim M, Fass D, (2009) Dimer interface migration in a viral sulfhydryl oxidase. J Mol Biol 391: 758-768.
11. Fischer MG, Allen MJ, Wilson WH, Suttle CA, (2010) Giant virus with a remarkable complement of genes infects marine zooplankton. Proc Natl Acad Sci USA 107: 19508-19513.
12. Arslan D, Legendre M, Seltzer V, Abergel C, Claverie JM, (2011) Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae. Proc Natl Acad Sci USA 108: 17486-17491.
13. Holm L, Rosenström P, (2010) Dali server: conservation mapping in 3D. Nucl Acids Res 38: W545-W549.
14. Wang J, Feng J-A, (2003) Exploring the sequence patterns in the α-helices of proteins. Prot Eng Des Sel 16: 799-807.
15. Jones DT, (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292: 195-202.
16. Fonseca NA, Camacho R, Magalhães AL, (2008) Amino acid pairing at the N- and C-termini of helical segments in proteins. Proteins 70: 188-196.
17. Vitu E, Bentzur M, Lisowsky T, Kaiser CA, Fass D, (2006) Gain of function in an ERV/ALR sulfhydryl oxidase by molecular engineering of the shuttle disulfide. J Mol Biol 362: 89-101.
18. Vala A, Sevier CS, Kaiser CA, (2005) Structural determinants of substrate access to the disulfide oxidase Erv2p. J Mol Biol 354: 952-966.
19. Legendre M, Audic S, Poirot O, Hingamp P, Seltzer V, et al. (2010) mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus. Genome Res 20: 664-674.
20. Raje S, Thorpe C, (2003) Inter-domain redox communication in flavoenzymes of the quiescin/sulfhydryl oxidase family: role of a thioredoxin domain in disulfide bond formation. Biochem 42: 4560-4568.
21. Heckler EJ, Alon A, Fass D, Thorpe C, (2008) Human quiescin-sulfhydryl oxidase, QSOX1: probing internal redox steps by mutagenesis. Biochem 47: 4955-4963.
22. Alon A, Grossman I, Gat Y, Kodali VK, DiMaio F, et al. (2012) The dynamic disulphide relay of quiescin sulfhydryl oxidase. Nature 488: 414-418.
23. Senkevich TG, Weisberg AS, Moss B, (2000) Vaccinia virus E10R protein is associated with the membranes of intracellular mature virions and has a role in morphogenesis. Virol 278: 244-252.
24. Rodríguez I, Redrejo-Rodríguez M, Rodríguez JM, Alejo A, Salas J, et al. (2006) African Swine Fever Virus pB119L protein is a flavin adenine dinucleotide-linked sulfhydryl oxidase. J Virol 80: 3157-3166.
25. Nie Y, Fang M, Theilmann DA, (2011) Autographa californica multiple nucleopolyhedrovirus core gene ac92 (p33) is required for efficient budded virus production. Virol 409: 38-45.
26. Unger T, Jacobovitch Y, Dantes A, Bernheim R, Peleg Y, (2010) Applications of the Restriction Free (RF) cloning procedure for molecular manipulations and protein expression. J Struct Biol 172: 34-44.
27. Van Duyne GD, Standaert RF, Karplus PA, Schreiber SL, Clardy J, (1993) Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin. J Mol Biol 229: 105-124.
28. Kabsch W, (2010) XDS. Acta Crystallogr D 66: 125-132.
29. Evans PR, (2005) Scaling and assessment of data quality. Acta Crystallogr D 62: 72-82.
30. Afonine PV, Grosse-Kunstleve RW, Adams PD (2005) The Phenix refinement framework. CCP4 Newsletter 42, contribution 8.
31. Emsley P, Cowtan K, (2005) Coot: model-building tools for molecular graphics. Acta Crystallogr D 60: 2126-2132.
32. Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, et al. (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D 54: 905-921.
33. Chen VB, Arendall WB 3rd, Headd JJ, Keedy DA, Immormino RM, et al (2010) MolProbity: all atom structure validation for macromolecular crystallography. Acta Crystallogr D 66: 12-21.